IKZF1 (Ikaros family zinc finger 1)

Written2000-08Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

1. Identity

Alias_names
General Information
ZNFN1A1
Alias_symbol (synonym)hIk-1
LyF-1
Hs.54452
IKAROS
PPP1R92
Other aliasIK1
LYF1
ZNFN1A1 (zinc finger protein, subfamily 1A, 1)
HGNC (Hugo) IKZF1
LocusID (NCBI) 10320
Atlas_Id 258
Location 7p12.2  [Link to chromosome band 7p12]
Location_base_pair Starts at 50304669 and ends at 50405100 bp from pter ( according to hg19-Feb_2009)  [Mapping IKZF1.png]
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
BCL6 (3q27.3) / IKZF1 (7p12.2)CREB3L2 (7q33) / IKZF1 (7p12.2)ENTPD1 (10q24.1) / IKZF1 (7p12.2)
IKZF1 (7p12.2) / ABCA13 (7p12.3)IKZF1 (7p12.2) / B2M (15q21.1)IKZF1 (7p12.2) / BCL6 (3q27.3)
IKZF1 (7p12.2) / CDK2 (12q13.2)IKZF1 (7p12.2) / ETV6 (12p13.2)IKZF1 (7p12.2) / IKZF1 (7p12.2)
IKZF1 (7p12.2) / LRBA (4q31.3)IKZF1 (7p12.2) / NUTM1 (15q14)IKZF1 (7p12.2) / POLR2A (17p13.1)
IKZF1 (7p12.2) / PRDM16 (1p36.32)IKZF1 (7p12.2) / SETD5 (3p25.3)IKZF1 (7p12.2) / TRPV2 (17p11.2)
IKZF1 (7p12.2) / ZEB2 (2q22.3)SETD5 (3p25.3) / IKZF1 (7p12.2)STIM2 (4p15.2) / IKZF1 (7p12.2)

2. DNA/RNA

Transcription 3629 bp mRNA; coding sequence: 1559 bp; 6 different splicings (--> 6 isoform proteins: ik1-ik6)

3. Protein

Description 519 amino acids; 58 kDa; possesses 2 Zinc-finger (C2H2-type) domains: one with 4 ZnF, the second with2 ZnF; DNA binding
Expression specificity for hematopoietic organs in the foetus and in the adult as well
Localisation nuclear
Function transcription regulator; can repress transcription through the recruitment of histone deacetylase complexes; role in conjunction with Aiolos; hemopoietic-specific zinc finger protein regulator of B and T-cell differentiation

4. Implicated in

Note
  
Entity t(3;7)(q27;p12) diffuse large B-cell lymphoma (DLCL) --> BCL6 / IKZF1
Note only 2 cases to date
Hybrid/Mutated Gene 5' Ikaros - 3' BCL6 fusion transcript; it is supposed that substitution of the promoter of BCL6 may be responsible for BCL6 deregulation
  

5. Bibliography

Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin.
Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, Fisher AG
Cell. 1997 ; 91 (6) : 845-854.
PMID 9413993
 
The role of the Ikaros gene in lymphocyte development and homeostasis.
Georgopoulos K, Winandy S, Avitahl N
Annual review of immunology. 1997 ; 15 : 155-176.
PMID 9143685
 
The Ikaros gene, a central regulator of lymphoid differentiation, fuses to the BCL6 gene as a result of t(3;7)(q27;p12) translocation in a patient with diffuse large B-cell lymphoma.
Hosokawa Y, Maeda Y, Ichinohasama R, Miura I, Taniwaki M, Seto M
Blood. 2000 ; 95 (8) : 2719-2721.
PMID 10753856
 
Ikaros interactions with CtBP reveal a repression mechanism that is independent of histone deacetylase activity.
Koipally J, Georgopoulos K
The Journal of biological chemistry. 2000 ; 275 (26) : 19594-19602.
PMID 10766745
 
Defects in hemopoietic stem cell activity in Ikaros mutant mice.
Nichogiannopoulou A, Trevisan M, Neben S, Friedrich C, Georgopoulos K
The Journal of experimental medicine. 1999 ; 190 (9) : 1201-1214.
PMID 10544193
 
Pre-T cell receptor (TCR) and TCR-controlled checkpoints in T cell differentiation are set by Ikaros.
Winandy S, Wu L, Wang JH, Georgopoulos K
The Journal of experimental medicine. 1999 ; 190 (8) : 1039-1048.
PMID 10523602
 
Identification of heterologous translocation partner genes fused to the BCL6 gene in diffuse large B-cell lymphomas: 5'-RACE and LA - PCR analyses of biopsy samples.
Yoshida S, Kaneita Y, Aoki Y, Seto M, Mori S, Moriyama M
Oncogene. 1999 ; 18 (56) : 7994-7999.
PMID 10637510
 

6. Citation

This paper should be referenced as such :
Huret, JL
IKZF1 (Ikaros family zinc finger 1)
Atlas Genet Cytogenet Oncol Haematol. 2000;4(4):179-180.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://atlasgeneticsoncology.usal.es/classic/Genes/IkarosID258.html

7. Other Leukemias implicated (Data extracted from papers in the Atlas) [ 12 ]

8. External links

Nomenclature
HGNC (Hugo)IKZF1   13176
LRG (Locus Reference Genomic)LRG_1121
Cards
AtlasIkarosID258
Entrez_Gene (NCBI)IKZF1  10320  IKAROS family zinc finger 1
AliasesCVID13; Hs.54452; IK1; IKAROS; 
LYF1; LyF-1; PPP1R92; PRO0758; ZNFN1A1
GeneCards (Weizmann)IKZF1
Ensembl hg19 (Hinxton)ENSG00000185811 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000185811 [Gene_View] &nbspENSG00000185811 [Sequence]  chr7:50304669-50405100 [Contig_View]  IKZF1 [Vega]
ICGC DataPortalENSG00000185811
TCGA cBioPortalIKZF1
AceView (NCBI)IKZF1
Genatlas (Paris)IKZF1
WikiGenes10320
SOURCE (Princeton)IKZF1
Genetics Home Reference (NIH)IKZF1
Genomic and cartography
GoldenPath hg38 (UCSC)IKZF1  -     chr7:50304669-50405100 +  7p12.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)IKZF1  -     7p12.2   [Description]    (hg19-Feb_2009)
EnsemblIKZF1 - 7p12.2 [CytoView hg19]  IKZF1 - 7p12.2 [CytoView hg38]
Mapping of homologs : NCBIIKZF1 [Mapview hg19]  IKZF1 [Mapview hg38]
OMIM603023   616873   
Gene and transcription
Genbank (Entrez)AF116605 AF180297 AF432219 AK303586 AK308411
RefSeq transcript (Entrez)NM_001220765 NM_001220766 NM_001220767 NM_001220768 NM_001220769 NM_001220770 NM_001220771 NM_001220772 NM_001220773 NM_001220774 NM_001220775 NM_001220776 NM_001291837 NM_001291838 NM_001291839 NM_001291840 NM_001291841 NM_001291842 NM_001291843 NM_001291844 NM_001291845 NM_001291846 NM_001291847 NM_006060
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)IKZF1
Cluster EST : UnigeneHs.731495 [ NCBI ]
CGAP (NCI)Hs.731495
Alternative Splicing GalleryENSG00000185811
Gene ExpressionIKZF1 [ NCBI-GEO ]   IKZF1 [ EBI - ARRAY_EXPRESS ]   IKZF1 [ SEEK ]   IKZF1 [ MEM ]
Gene Expression Viewer (FireBrowse)IKZF1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets] &nbsp [Normal Tissue Atlas] &nbsp[carcinoma Classsification] &nbsp[NCI60]
GenevestigatorExpression in : [tissues] &nbsp[cell-lines] &nbsp[cancer] &nbsp[perturbations] &nbsp
BioGPS (Tissue expression)10320
GTEX Portal (Tissue expression)IKZF1
Human Protein AtlasENSG00000185811-IKZF1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13422   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ13422  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13422
Splice isoforms : SwissVarQ13422
PhosPhoSitePlusQ13422
Domaine pattern : Prosite (Expaxy)ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (EBI)Znf_C2H2_sf    Znf_C2H2_type   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Domain families : Smart (EMBL)ZnF_C2H2 (SM00355)  
Conserved Domain (NCBI)IKZF1
DMDM Disease mutations10320
Blocks (Seattle)IKZF1
SuperfamilyQ13422
Human Protein Atlas [tissue]ENSG00000185811-IKZF1 [tissue]
Peptide AtlasQ13422
HPRD04318
IPIIPI00013232   IPI00216387   IPI00216388   IPI00216389   IPI00216390   IPI00216391   IPI00216392   IPI00782995   IPI01011333   IPI00152529   IPI00926847   
Protein Interaction databases
DIP (DOE-UCLA)Q13422
IntAct (EBI)Q13422
FunCoupENSG00000185811
BioGRIDIKZF1
STRING (EMBL)IKZF1
ZODIACIKZF1
Ontologies - Pathways
QuickGOQ13422
Ontology : AmiGODNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA binding  DNA-binding transcription factor activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  chromatin organization  cell cycle  mesoderm development  protein domain specific binding  lymphocyte differentiation  erythrocyte differentiation  nuclear pericentric heterochromatin  protein-containing complex  protein-containing complex  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  metal ion binding  protein heterooligomerization  
Ontology : EGO-EBIDNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA binding  DNA-binding transcription factor activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  chromatin organization  cell cycle  mesoderm development  protein domain specific binding  lymphocyte differentiation  erythrocyte differentiation  nuclear pericentric heterochromatin  protein-containing complex  protein-containing complex  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  metal ion binding  protein heterooligomerization  
NDEx NetworkIKZF1
Atlas of Cancer Signalling NetworkIKZF1
Wikipedia pathwaysIKZF1
Orthology - Evolution
OrthoDB10320
GeneTree (enSembl)ENSG00000185811
Phylogenetic Trees/Animal Genes : TreeFamIKZF1
HOGENOMQ13422
Homologs : HomoloGeneIKZF1
Homology/Alignments : Family Browser (UCSC)IKZF1
Gene fusions - Rearrangements
Fusion : MitelmanIKZF1/ABCA13 [7p12.2/7p12.3] &nbsp
Fusion : MitelmanIKZF1/BCL6 [7p12.2/3q27.3] &nbsp[t(3;7)(q27;p12)]  
Fusion : MitelmanIKZF1/LRBA [7p12.2/4q31.3] &nbsp[t(4;7)(q31;p12)]  
Fusion : MitelmanIKZF1/PRDM16 [7p12.2/1p36.32] &nbsp[t(1;7)(p36;p12)]  
Fusion PortalIKZF1 7p12.2 LRBA 4q31.3 BRCA
Fusion : TICdbIKZF1 [7p12.2]  -  BCL6 [3q27.3]
Fusion : QuiverIKZF1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerIKZF1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)IKZF1
dbVarIKZF1
ClinVarIKZF1
1000_GenomesIKZF1 
Exome Variant ServerIKZF1
ExAC (Exome Aggregation Consortium)ENSG00000185811
GNOMAD BrowserENSG00000185811
Varsome BrowserIKZF1
Genetic variants : HAPMAP10320
Genomic Variants (DGV)IKZF1 [DGVbeta]
DECIPHERIKZF1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisIKZF1 
Mutations
ICGC Data PortalIKZF1 
TCGA Data PortalIKZF1 
Broad Tumor PortalIKZF1
OASIS PortalIKZF1 [ Somatic mutations - Copy number]
Cancer Gene: CensusIKZF1 
Somatic Mutations in Cancer : COSMICIKZF1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDIKZF1
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch IKZF1
DgiDB (Drug Gene Interaction Database)IKZF1
DoCM (Curated mutations)IKZF1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)IKZF1 (select a term)
intoGenIKZF1
NCG5 (London)IKZF1
Cancer3DIKZF1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603023    616873   
Orphanet21584    10430    14433   
DisGeNETIKZF1
MedgenIKZF1
Genetic Testing Registry IKZF1
NextProtQ13422 [Medical]
TSGene10320
GENETestsIKZF1
Target ValidationIKZF1
Huge Navigator IKZF1 [HugePedia]
snp3D : Map Gene to Disease10320
BioCentury BCIQIKZF1
ClinGenIKZF1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10320
Chemical/Pharm GKB GenePA37748
Clinical trialIKZF1
Miscellaneous
canSAR (ICR)IKZF1 (select the gene name)
DataMed IndexIKZF1
Probes
Litterature
PubMed260 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineIKZF1
EVEXIKZF1
GoPubMedIKZF1
iHOPIKZF1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Jan 17 18:58:02 CET 2019

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